Groundwater contamination is of environmental and human health concern. Bioremediation is a nature-based method for contaminant treatment. Bioremediation, which relies on the ability of microorganisms to destroy or transform contaminants, must be reliable and cost-competitive in comparison to more traditional treatment methods. Two hurdles must be overcome to enhance bioremediation’s effectiveness and competitiveness: i) being able to degrade recalcitrant compounds, and ii) being able to control the growth rate and location of microorganisms involved in bioremediation in the subsurface. My dissertation adds foundational knowledge and engineering application on how to biodegrade recalcitrant emerging and legacy halogenated compounds. Generating biotransformation knowledge on the recalcitrant emerging contaminants called per- and polyfluoroalkyl substances (PFAS) may lead to solutions for protecting both people and the planet. In my dissertation, I analyzed PFAS biotransformation and microbial defluorination literature via meta-analytical and bibliometric methods to identify unexplored topics and experimental conditions. The metanalytical work identified trends in PFAS microbial biotransformation science to inform future experimental design. The second hurdle which must be overcome is being able to control bacterial growth in the subsurface. During bioremediation implementation microbial overgrowth may clog injection wells and the subsurface, leading to reduced porosity and treatment efficacy. Contaminant treatment schemes based on aerobic cometabolism frequently exhibit overgrowth at subsurface injection points for O2 (the electron acceptor) and a labile hydrocarbon (e.g., propane). My dissertation work experimentally evaluated acetylene as a microbial inhibitor for use in controlling microbial overgrowth during trichloroethene (TCE) aerobic cometabolism. I demonstrated that acetylene reduces the likelihood of microbial overgrowth of TCE-degrading microorganisms in soil-free microcosms and aquifer soil columns while retaining TCE degradation capacity. Cumulatively, my dissertation provides foundational knowledge for academics and bioremediation practitioners to develop robust and reliable bioremediation technologies.

Chlorinated ethenes are among the most prevalent legacy contaminants affecting groundwater quality. A common treatment for chlorinated ethenes in the subsurface is in situ anaerobic bioremediation where the organohalide-respiring bacteria, Dehalococcoides mccartyi, convert the contaminants to non-toxic ethene via hydrogen (H2) dependent reductive dehalogenation. Typically, D. mccartyi obtain H2 through the fermentation of organic substrates by fermentative bacteria. However, stimulation of H2 competing processes causing production of methane (a potent greenhouse gas), rapid substrate consumption of simple substrates, and well/pore clogging by viscous complex substrates often challenge bioremediation, leading to slow rates of dehalogenation or stalls at chlorinated intermediates.This dissertation details the potential of microbial chain elongation as a technology for bioremediation of chlorinated ethenes. In chain elongation, bacteria reliably produce H2 and carboxylates (e.g., butyrate (C4)) using simple compounds (e.g., ethanol (C2) and acetate (C2)) as substrates. Under certain conditions, production of alcohols (e.g., butanol (C4)) can also occur. Here, chain elongation was demonstrated to drive reductive dehalogenation of trichloroethene via direct rapid-release H2 and slow-release H2 during fermentation of elongated products. Results showed chain elongation suppressed methanogenesis, supporting chain elongation as a potential solution for bioremediation when typical fermentable substrates do not meet treatment goals. Next, the potential for chain elongation was evaluated using groundwater and soil from a Superfund site experiencing challenges with bioremediation. Soils from the site were found to contain chain elongating bacteria, while groundwater not previously stimulated with ethanol and acetate was steered to chain elongate with bioaugmentation. Additional chain elongation substrate combinations relevant to bioremediation were identified. Results are being used to inform the design of a pilot study at the site. Lastly, this research identified and demonstrated higher ethanol concentrations, higher total pressures, and higher H2 partial pressure improves chain elongation activity and production of butanol, an important biofuel. These results aid in efforts to make chain elongation relevant as a bioprocess in a circular economy and bioremediation. Cumulatively, this dissertation research demonstrated the potential of chain elongation in bioremediation of chlorinated ethenes, indicating it should be considered when evaluating solutions for contaminated sites.

Oxic beds containing basic oxygen furnace slag were evaluated as potential post-treatment method for sulfate reducing bioreactor (SRB) treatment of acid rock drainage. SRB effluent was pumped into BOF slag/sand leach beds, also known as oxic slag beds (OSBs), at various flow rates. OSB influent versus effluent concentrations of dissolved metals (specifically magnesium and manganese) and water quality parameters (pH, dissolved oxygen concentration, and conductivity) were compared. The OSBs increased the pH of the SRB effluents from 6.2–6.7 to 7.5–8.3. Dissolved oxygen concentration increased from 2-4 mg L^(-1) to approximately 8 mg L^(-1). Conductivity remained similar, with some effluent values being less than influent. Manganese concentration was observed to be reduced through OSB post-treatment by an average of 8.2% reduction and a maximum of 23 % reduction. Magnesium was not reduced during OSB post-treatment. Other metal concentrations changes were analyzed. Recommendations the design of OSBs for future studies were made, and a proposed design was configured.

The objective of this study was to evaluate possible bioremediation strategy for aerobic aquifers by combining ZVI chemical reduction and microbial reductive dechlorination for TCE and ClO4-. To achieve this objective, continuous flow-through soil columns were used to test the hypothesis that bioaugmentation with dechlorinating enrichment cultures downstream of the ZVI injection can lead to complete reduction of TCE and ClO4- in aerobic aquifers. We obtained soil and groundwater from a Superfund site in Arizona. The experiments consisted of 205 cm3 columns packed with soil and ZVI, which fed 1025 cm3 columns packed with soil, biostimulated with fermentable substrates and bioaugmented. Aerobic groundwater was pumped through the ZVI columns. The ZVI reduced the oxidation-reduction potential (ORP) of groundwater from +150 mV to -190 mV. The reduced groundwater and biostimulation with fermentable substrates created anaerobic conditions in the bioaugmentation columns favorable for anaerobic microbial activity. Perchlorate (ClO4-) reduction to non-detectable levels occurred after biostimulation. Reduction of TCE to cis-dichloroethene, vinyl chloride and ethene was observed only after bioaugmentation. Within ~120 days of continuous columns operation, ethene was produced in the bioaugmentation columns this dechlorination activity was sustained until the end of experiments. The groundwater from the Superfund site had high concentration of sulfate (~1000 mg/L). Substantial sulfate reduction occurred in the bioaugmentation columns. Complete microbial reduction of TCE and perchlorate is usually challenging in the presence of high sulfate concentration; however, the strategy tested in this study suggests that a bioremediation scheme for simultaneous reduction of TCE and perchlorate in aerobic aquifers containing high sulfate concentration is feasible.

Trichloroethene (TCE) is a ubiquitous soil and groundwater contaminant. The most common bioremediation approach for TCE relies on the process of reductive dechlorination by Dehalococcoides mccartyi. D. mccartyi use TCE, dichloroethene, and vinyl chloride as electron acceptors and hydrogen as an electron donor. At contaminated sites, reductive dechlorination is typically promoted by adding a fermentable substrate, which is broken down to short chain fatty acids, simple alcohols, and hydrogen. This study explored microbial chain elongation (MCE), instead of fermentation, to promote TCE reductive dechlorination. In MCE, microbes use simple substrates (e.g., acetate, ethanol) to build medium chain fatty acids and also produce hydrogen during this process. Soil microcosm using TCE and acetate and ethanol as MCE substrates were established under anaerobic conditions. In soil microcosms with synthetic groundwater and natural groundwater, ethene was the main product from TCE reductive dechlorination and butyrate and hydrogen were the main products from MCE. Transfer microcosms using TCE and either acetate and ethanol, ethanol, or acetate were also established. The transfers with TCE and ethanol showed the faster rates of reductive dechlorination and produced more elongated products (i.e., hexanoate). The microbial groups enriched in the soil microcosms likely responsible for chain elongation were most similar to Clostridium genus. These investigations showed the potential for synergistic microbial chain elongation and reductive dechlorination of chlorinated ethenes.

On average, our society generates ~0.5 ton of municipal solid waste per person annually. Biomass waste can be gasified to generate synthesis gas (syngas), a gas mixture consisting predominantly of CO, CO2, and H2. Syngas, rich in carbon and electrons, can fuel the metabolism of carboxidotrophs, anaerobic microorganisms that metabolize CO (a toxic pollutant) and produce biofuels (H2, ethanol) and commodity chemicals (acetate and other fatty acids). Despite the attempts for commercialization of syngas fermentation by several companies, the metabolic processes involved in CO and syngas metabolism are not well understood. This dissertation aims to contribute to the understanding of CO and syngas fermentation by uncovering key microorganisms and understanding their metabolism. For this, microbiology and molecular biology techniques were combined with analytical chemistry analyses and deep sequencing techniques. First, environments where CO is commonly detected, including the seafloor, volcanic sand, and sewage sludge, were explored to identify potential carboxidotrophs. Since carboxidotrophs from sludge consumed CO 1000 faster than those in nature, mesophilic sludge was used as inoculum to enrich for CO- and syngas- metabolizing microbes. Two carboxidotrophs were isolated from this culture: an acetate/ethanol-producer 99% phylogenetically similar to Acetobacterium wieringae and a novel H2-producer, Pleomorphomonas carboxidotrophicus sp. nov. Comparison of CO and syngas fermentation by the CO-enriched culture and the isolates suggested mixed-culture syngas fermentation as a better alternative to ferment CO-rich gases. Advantages of mixed cultures included complete consumption of H2 and CO2 (along with CO), flexibility under different syngas compositions, functional redundancy (for acetate production) and high ethanol production after providing a continuous supply of electrons. Lastly, dilute ethanol solutions, typical of syngas fermentation processes, were upgraded to medium-chain fatty acids (MCFA), biofuel precursors, through the continuous addition of CO. In these bioreactors, methanogens were inhibited and Peptostreptococcaceae and Lachnospiraceae spp. most likely partnered with carboxidotrophs for MCFA production. These results reveal novel microorganisms capable of effectively consuming an atmospheric pollutant, shed light on the interplay between syngas components, microbial communities, and metabolites produced, and support mixed-culture syngas fermentation for the production of a wide variety of biofuels and commodity chemicals.